The Parks Department is seeking a new operator for a high-grossing restaurant and banquet hall in Queens after a scathing audit by Comptroller Bill Thompson questioned whether the current operator was reporting all its revenues, officials said yesterday.

The agency said it would sever its contract with Merissa Restaurant Corp. – which has been running Caffe on the Green since 1992 – in February.

That’s one year before the scheduled expiration.

Thompson’s auditors determined the eatery owes the city $120,607 in additional license fees and late penalties for 2006 and 2007.

But the auditors said they were far more disturbed by the shoddy bookkeeping. Five of 12 guest checks were “not correctly reported on point-of-sales contracts,” while 23 of 66 banquets “had at least one recording irregularity,” according to the audit.

Parks officials said they’re going to recoup the entire $120,607 and are also looking for a new restaurateur.

The Bayside operation takes in nearly $5 million a year.

The Parks Department receives 10 percent because it owns the facility, a mansion that was once home to Rudolph Valentino and Mayor Fiorello La Guardia.